When converting a Markdown document to PDF with pandoc, my images are not placed in the same position I put them in the source code. I believe this is due to the conversion
Did you try to deactivate the implicit_figures as in
implicit_figures
pandoc -f markdown-implicit_figures -t pdf myfile.md
To solve the size problem you could also try to fix the size within the markdown file with an attribute. Something like that can do the trick:
{ width=50% }